The Flash: The truth behind Dr Wells
by bloomscool
Summary: Do you ever wonder what will happen when they figure Dr. Wells out? Will he reveal himself? Will the others reveal him? Read this to find out just one of the million ways the truth can come out but just remember...the truth doesn't set everyone free.
1. Chapter 1

**This story is about everything changing, ok Iris and Wally know Barry's secret and Iris is currently dating Barry, disclaimer I own nothing. **

Cisco was walking down the dark alleyway, he hated going down this alleyway but it was the quickest way to the movie theatre, besides he had his phone on him so he could call his buddy the Flash aka Barry Allen if he was in trouble. He looked back a few times because he kept hearing stuff like someone walking behind him and once he thought he heard someone breathing right behind him, he sighed, "I'm so getting a new shortcut, one that's less creepy." He moved on, he really wished there was more lighting in the alleyways, especially at night, oh well at least the area is lit up enough for him to see his feet. He saw a figure up ahead, the figure was lying down and looked familiar, he ran up to the figure and gasped, it was Dr. Wells!

He had a large gash on his head, a black eye, Cisco couldn't help but notice how weird he looked without glasses, Dr. Wells looked up at Cisco and said, "Cisco, h-h-help m-m-m-me."

Cisco got down to his level and asked, "Sir, who did this to you?" Dr. Wells was the boss and head scientist of S.T.A.R labs, about a year earlier his particle accelerator malfunctioned and well let's just say that due to that accident Barry Allen was gifted with super speed.

Suddenly a man with a blurry face, yellow costume, and red eyes ran right in between them, Dr. Wells whispered, "Cisco, run, he's going to kill you. Leave me here and run."

Cisco shook his head and replied, "No, I'm not leaving you with this madman." Cisco reached into his pocket for his phone but found that he couldn't find it, he looked up and saw that the man in the yellow suit had his phone; he held it up and crushed it in his hands. This wasn't good; this man is called the Reverse Flash and when Barry was eleven years old Reverse Flash killed his mother, Nora Allen, with a knife.

He picked up a metal pole and said, "I will use this." Dr. Wells pushed himself up slightly with his arms and exclaimed, "Cisco, just run!" So that's what he did but he didn't get very far, of course he didn't get very far this was the Reverse Flash, he tried hitting the speedster with the pole but he just grabbed it and ripped it right out of his hands, the speedster then began running around him. Cisco was getting scared, this is what happened to Nora Allen the night she died, he wondered how Barry felt, what he was thinking when it happened. He looked at Dr. Wells, he was hopeful that Reverse Flash would spare the man's life, Dr. Wells lost the use of his legs after the particle accelerator explosion so he couldn't run away. He remembered the day Dr. Wells found him, it was after he graduated college, Dr. Wells had been impressed with how he made a drill that could fire a laser strong enough to cut through thick wood like soft butter so he offered him a job at S.T.A.R labs, since then Dr. Wells had become a sort of father figure to him which is why, after the accident, he came back to help Dr. Wells try to get S.T.A.R labs back on the map. Reverse Flash sped up, he wasn't speaking but Cisco knew the speedster was taunting him, waiting for Cisco to break down, he wasn't going to though, he was going to stand strong.

Dr. Wells watched in horror and whispered, "Cisco."

He couldn't save the young man though, Cisco looked at his friend and said, "You can do anything you want to me but please, spare Dr. Wells' life." Cisco wished he could he could get away from Reverse Flash but he knew he couldn't, suddenly it all stopped, the running stopped, Dr. Wells suddenly faded away, now a cloth with chloroform on it was being shoved into the young man's face, that was when his whole world went dark, Reverse Flash threw the unconscious Cisco over his shoulder and sped away.

* * *

Caitlin was putting a light red jacket on, she was in her apartment and waiting for Barry in the living room, they were going to the movies with Iris, Cisco, and Wally, the fifteen year old who only found out who Barry was by accident. Caitlin got a quick drink of water but felt like she was forgetting something, she face palmed and sighed, "I almost forgot, I'm going to need a few extra dollars, between Barry's hyperactive metabolism and Cisco's sweet tooth I'm not going to have enough money for my own snacks. And I have to put my lipstick on and I can't forget the necklace Ronnie gave me." It took a few months and while Ronnie still didn't remember anything he decided to stick around and help the Flash out, he was busy at the lab though so he couldn't go with the others to watch the movie. She went back to her room and got another one hundred dollars out of under her mattress, after super powered criminals started robbing banks she decided to take Cisco's advice and put her money under safe places like mattresses, in her sock drawers, places like that.

She heard a slight rustle come from her closet and noted, "I'm going to have to tell the landlord that there are mice in my apartment…**again**." She looked in the mirror and decided to skip the lipstick and necklace this time, besides it's just going to be a casual meeting between friends, although it'll turn into an intervention with Cisco about his choice of shortcuts to places like movie theatres.

She went to get her phone from the top of her dresser but saw that it was missing; she heard that familiar demonic voice say, "Hello, you must be Caitlin."

She turned around and gasped, it was the Reverse Flash, she stepped back slightly and asked, "W-what are you doing here?"

He stepped forward slightly and replied, "Just here to give you a gift."

She stepped back a little bit more and said, "That's nice, so what's my gift?"

He grabbed her arm and replied, "Nuh-uh nope, that's a surprise Caitlin, I'll give you a little preview though."

He ran and tore the sheets off her bed, ran another way and knocked some random stuff over, she nervously asked, "What are you doing?"

He ran into the living room for a brief moment and after he knocked some more stuff around he came back and replied, "I'm making it look like you were able to put up a small fight against me." He grabbed her arm and put a cloth with chloroform on it over her face then threw her over his shoulder and sped off.

* * *

Barry ran Iris and Wally to the front door of Caitlin's apartment; Iris got off Barry's back and asked, "You do know that we could've just driven here right?"

As she smoothed her hair back down Barry grinned and replied, "I know but Wally wanted me to carry him and use my super speed."

She turned to her nephew and asked, "Did you enjoy the ride?" Wally grinned and nodded, it was silly really how he found out about Barry's secret, he walked into Barry's room and saw him putting his laundry away with his super speed.

Iris chuckled and said, "At least his new Batman t-shirt isn't on fire like with what happened to Felicity."

Barry blushed and asked, "How do you know about that?"

Iris tucked her hair behind her ear and replied, "Felicity told me after I learned your secret." Felicity is an old friend from Starling City and partner to Oliver Queen aka the Arrow, Barry chuckled at the memory of that day and opened the door and gasped, Iris stepped in and gasped to,

Wally walked in and wondered, "What happened in here? It looks like a tornado swept through here." Barry noticed the phone on the kitchen counter and instantly knew something was wrong, Caitlin never goes anywhere without her phone,

Barry turned to his girlfriend and Wally and said, "Stay here, I'm going to search Caitlin's room." He ran to her room and stared in pure terror, the bed sheets were thrown on the ground, the clock was on the floor, her makeup was all over the place. He hurried to the others;

Iris saw the worry on his face and asked, "What did you find?"

Barry took in a deep breath and replied, "Whatever happened here that caused Caitlin to vanish, whoever took Caitlin, put up a fight against her the moment she resisted. I think it started in her bedroom."

He was panicking now, a new enemy or an old enemy has taken Caitlin, he tried calling Cisco but he wasn't answering, Iris put a hand on her boyfriend's shoulder and said, "Hun it'll be alright, let's head to S.T.A.R labs and try to figure out what happened. Ronnie will help us; he's still at the lab."

He nodded and asked, "Wally, do you want to see S.T.A.R labs?"

Wally grinned and replied, "Of course!" Barry just hoped that his friends were alright.

* * *

Cisco woke up and found himself inside some kind of energy field, he looked around to see that he was on a platform several feet in the air, he then saw Caitlin in a cage that was dangling above a vat of some kind of chemical,

Caitlin woke up and looked at Cisco and asked, "Cisco, are you ok?"

Cisco nodded and replied, "I am but Caitlin, whatever you do, don't look down."

Caitlin raised an eyebrow and asked, "Why what's wrong?"

He took a deep breath and replied, "Just don't look down."

Curiosity got the better of her and she nervously looked down, she deeply regretted it, she screamed in terror then looked up and asked, "What is this?"

Cisco noticed something on the glass and replied, "If that writing is correct you have been suspended over liquid nitrogen." Caitlin started to panic, there was no way out of this, she was going to die, she began crying over the fact that she was never going to see Ronnie again.

Cisco stood up and said, "Caitlin you have to calm down, we will get through this, somehow, come on let's talk about something else for a bit."

Caitlin nodded and replied, "Ok, how did you get kidnapped?"

Cisco explained what happened in the ally, Caitlin worriedly asked, "Is Dr. Wells ok?"

Cisco shrugged and replied, "I don't know, before I passed out he vanished. Don't know how it happened, he just vanished."

A demonic voice said, "Good, you two are awake."

Reverse Flash appeared in front of them, Cisco asked, "What do you want from us?"

Reverse Flash looked directly at him and replied, "Well, right now I only want to make demands from Barry but after the video conference is over…well you'll see."

Caitlin glared and asked, "Who are you behind the mask?" Suddenly his voice stopped sounding demonic and began sounding…familiar, he replied, "Haven't you guessed it by now? I thought we were friends." He took the mask off and stopped vibrating to reveal himself as Dr. Wells! They gasped in surprise, they couldn't believe it, the man they admired and respected was really the Reverse Flash, but they were also so confused. Why did he do what he did, why did he kill so many innocent people,

Caitlin shook her head and asked, "How-what-why are you doing this?"

Dr. Wells smiled and replied, "I made that clear, I'm using you two against Barry." Those words cut them like a knife;

Dr. Wells looked at Cisco and asked, "Is there anything you'd like to ask?"

Cisco crossed his arms and replied, "Just one question for now, why did you pick us back then?"

Dr. Wells smirked and explained, "I was using you Cisco, Caitlin, using you both to make Barry stronger, right now I'm using you both as leverage against Barry and as tools. Don't worry, you'll both have served your purpose soon enough." It was painful to hear this, this came from the man that they all respected and admired for years, the moment he asked for their help they stopped everything else and returned as quickly as possible to his side, they could've just said no but they wanted to come and help their father figure. Now he was saying that he was just using them, he didn't care if they died,

Caitlin stood up and asked, "But how did you appear in two places at once?"

He turned around, put his mask back on, and replied, "All will be explained soon Caitlin."

* * *

Barry began pacing at super speed; Joe walked into the lab and asked, "Has there been any update?"

Iris hugged her dad and replied, "Not yet, all we know is that Caitlin was kidnapped almost an hour ago and that we are pretty sure Cisco was kidnapped to, he's not answering his phone."

Joe nodded then asked, "Do we have any suspects?"

Barry stopped pacing and replied, "That's the problem there are too many suspects who would love to get to me by harming my friends, most of which are metahumans or have weapons that can kill anyone within seconds."

Ronnie put a hand on his shoulder and said, "Barry, think, who would be able to pull this off? Who would have the kind of patience to memorize every detail of your friends' lives and would kidnap them like this just to freak you out? I know a lot of your enemies are patient observers but think…who would trash Caitlin's apartment to make it look like a struggle?"

Barry raised an eyebrow and asked, "What do you mean someone trashed Caitlin's apartment to make it look like a struggle?"

Wally sat on a chair backwards and replied, "Didn't you notice? Everything was knocked around but not broken; it looked like whoever did this was making it look like a horrible struggle to scare someone." Barry's eyes widened in realization, how had he missed that? He was so caught up in fear that he didn't pay attention to the minute details.

He took a deep breath and said, "Truthfully I'm not sure who would do this or at least be able to, Captain Cold has the ability to do this but we have a sort of non-aggression treaty going, as long as he stays away from my friends and family and doesn't kill anyone…we have a drink as buds at the bar every once in a while." It was true, Captain Cold was originally a killer but after joining up with some other villains he realized the horrible things he did and took a level in kindness, he's still a villain but he's nicer and just tries to scare and not kill people as cheesy as that sounds. He couldn't think of anyone else with that kind of patience except maybe Reverse Flash, oh how he hoped it wasn't Reverse Flash.

He continued, "But…there is a possibility that Reverse Flash did this but I don't know you'd think he'd at least leave a note or something."

Wally looked at the computer he was in front of and said, "Guys, someone's calling us." He clicked a button and it brought up a video of Cisco inside an energy bubble and Caitlin was in a cage hanging over a vat of liquid nitrogen just a few feet away from Cisco.

Barry exclaimed, "Caitlin, Cisco!" Fear and relief washed over Barry, relief that they weren't dead but fear that they'd be very close to it, suddenly the man he feared was behind all of this appeared on the screen but the man wasn't vibrating his face.

Reverse Flash took the mask off and said in his demonic voice, "Hello Barry."

He gasped, it was the man he admired for almost a year, Dr. Wells, the man was smirking as Barry whispered silently, "No…"

**Well that was interesting, I hope you enjoy this and please no flames; this is my first Flash story so take it easy on me.**


	2. Chapter 2, explanation and complication

**First of, Wally doesn't exist in the show yet but he's important to the story, this time w****e're going to get explanations but also some complications, disclaimer I own nothing. And sorry this took so long, I wanted a logical explanation for this so I waited then before I knew it bam the series ended, oh well think of this as an AU…like you already are…on with the story.**

Wally got out of the chair so that Barry could sit; Barry glared at the man on the screen and asked, "Why did you do this? How did you do this?"

Dr. Wells smirked at the young man's anger and fear as he explained, "There was a man from Gotham named John Marlowe who created a device that could duplicate anything, even humans, I stole the device to make the duplicate so that you would think the Reverse Flash was someone else. Now as for why, well you'll find out soon."

Barry growled slightly and said, "I **will **find you Wells." Dr. Wells laughed and replied, "No you won't you see if you try to find me I'll kill your friends with this button."

He held up a small box with various buttons on it, fear washed over Barry like a tidal wave, he didn't let it show though as he asked, "What do you want?" Dr. Wells was still smirking as he replied, "Simple you will wait seventy two hours, after that time is up I will give you the time and location, understand that if you are late I will get bored and kill your friends. I don't want money, all I want is to fight you one on one, if you choose to do this I will give you your friends back but if you don't then well…let's just say that I'll have a lot of fun with them. Another thing, if you try to come here early I'll kill them so wait and train for our fight Barry."

Then the screen faded to black, Barry slammed a fist on the desk and exclaimed, "No!"

Iris put a hand on her shoulder and said, "Barry, calm down. Freaking out isn't healthy for anyone especially not now." She turned to Ronnie and continued, "Ronnie, take Barry into the training area and help him get ready, Wally you go to."

Wally nodded and said, "Alright, come on Ronnie, Uncle Barry."

After they left Iris asked, "Dad, what can we do?"

Her dad sighed and replied, "Iris…there's not much we can do, we just have to hope that Wells will keep his promise."

Cisco sat, watching Dr. Wells run on his treadmill at super speed, once he stopped Dr. Wells noted, "You have no idea how great it feels to run like this, I started to fear that I forgot how to run what with the whole wheelchair act."

Dr. Wells pressed a button that made two prods come out on both sides of the force field, the prods dug into Cisco's body and he screamed as electricity crackled over his body. Caitlin's eyes went wide in horror as she exclaimed, "Cisco!"

After about ten seconds the prods went back outside the force field and she asked, "Why did you do that?"

He sat in a metal chair and replied, "Just making sure he stays awake."

"Awake for what?"

"Awake for my **manual labor** and unlike some famous Let's Players on YouTube I will not be enjoying it…ok maybe I enjoy this kind of manual labor a little."

Cisco leaned against the energy field and asked, "What manual labor are you doing?"

Wells crossed his arms and nonchalantly replied, "This kind."

The speedster smiled as the prods dug into Cisco again, Caitlin had a hint of anger in her voice as she asked, "Why are you doing this?"

Dr. Wells sat on his chair and explained, "I'm from the future, I tried to kill Barry as a child but the future Barry had the gall to stop me so…I killed Nora Allen."

"Yeah, **Barry** was the one who had the gall."

Cisco screamed as the prods electrocuted him again for that comment, Wells stopped the prods and continued, "**Anyways**, I messed up slightly and made it so that Martian Manhunter would never save Wally West's parents two months ago during the ski incident because he's still on Mars drinking Martian tea. I'll explain that later but anyways I also messed with human evolution by preventing Tess from meeting Mark and Marie Logan to discuss genetics research and thus she never made the mini prototype particle accelerator and thus it never exploded and the explosion never covered this entire planet and would've allowed anyone to become a Meta human. All because I killed Tess that same night I killed Nora."

Caitlin gave a disgusted look, "You killed your own wife."

Wells shook his head and laughed a little, "Actually I killed her husband alongside her and assumed his ID."

Cisco wiped some sweat away and asked, "Who are you really then?"

The prods dug into his skin again as Dr. Wells replied, "Another day for that story Cisco."

Wally was running on the treadmill, Ronnie walked in and asked, "What're you doin little buddy?"

Wally stopped running and replied, "Trying to get as fast as Uncle Barry, he'll need all the help he can get."

Ronnie smiled and said, "That's a wonderful thing you're trying but...you can't get super speed like Barry…although I do need some help. Felicity, Ray, and Oliver are bringing over someone who might be able to help us. I need you to help move some medical supplies, the guy they're bringing over isn't a fan of labs so we have to make the place seem inviting."

Wally nodded and as they moved the boxes he asked, "Who are they bringing over?"

Ronnie sat the box on a shelf and replied, "Never met him, whoever he is he's supposedly a genius in the field of genetics. He's studying Meta genes you know the thing that gives humans powers."

Wally paused, "Huh, mostly the bad guys have been studying Meta genes." Ronnie nodded and replied, "And that is why we're lucky to have him on our side. He's apparently found something important out about our super powers."

Barry, Joe, and Iris walked in with a banner that had _Welcome to our lab! _Written on it, as they hung it onto the ceiling Iris excitedly said, "They'll be here in five minutes, Barry tie the balloons to the chairs."

Barry nodded and replied, "On it!"

Joe looked around and asked, "Isn't this a bit…I don't know…excessive?"

After Barry was done tying the balloons to the chairs he replied, "We just want to make this place homey for the new scientist, this information he has might help us someday." Soft piano music started playing in the background and they turned to see Ronnie grinning while standing next to a stereo. Joe shrugged and got out a bottle of Champaign as the door opened, their friends began to step through the door.

"**SURPRISE!**"

**Guess who the scientist is. It'll blow your mind who he is, hint, he is not Martin Stein but the new scientist will contribute to that discovery and he's someone from the comics, in those comics he wasn't a scientist, and he's on of my top five favourite DC heroes, at least for the boys side. Also I hope you got the reference to the YouTuber Chuggaaconroy and the Martian tea reference from Young Justice. **


End file.
